A simple tool for stereological assessment of digital images: the STEPanizer

STEPanizer is an easy‐to‐use computer‐based software tool for the stereological assessment of digitally captured images from all kinds of microscopical (LM, TEM, LSM) and macroscopical (radiology, tomography) imaging modalities. The program design focuses on providing the user a defined workflow adapted to most basic stereological tasks. The software is compact, that is user friendly without being bulky. STEPanizer comprises the creation of test systems, the appropriate display of digital images with superimposed test systems, a scaling facility, a counting module and an export function for the transfer of results to spreadsheet programs. Here we describe the major workflow of the tool illustrating the application on two examples from transmission electron microscopy and light microscopy, respectively.

[1]  M J Puddephat,et al.  The benefit of stereology for quantitative radiology. , 2000, The British journal of radiology.

[2]  H. J. G. Gundersen,et al.  The new stereological tools: Disector, fractionator, nucleator and point sampled intercepts and their use in pathological research and diagnosis , 1988, APMIS : acta pathologica, microbiologica, et immunologica Scandinavica.

[3]  C. Saper,et al.  Any way you cut it: A new journal policy for the use of unbiased counting methods , 1996, The Journal of comparative neurology.

[4]  P. R. Hof,et al.  Design-based stereology in neuroscience , 2005, Neuroscience.

[5]  P. Burri,et al.  Effects of Mild Vitamin A Deficiency on Lung Maturation in Newborn Rats: A Morphometric and Morphologic Study , 2004, Neonatology.

[6]  E B Hunziker,et al.  Stereology for anisotropic cells: Application to growth cartilage * , 1986, Journal of microscopy.

[7]  Mayhew Tm,et al.  The new stereological methods for interpreting functional morphology from slices of cells and organs , 1991, Experimental physiology.

[8]  T. Mayhew,et al.  Taking tissue samples from the placenta: an illustration of principles and strategies. , 2008, Placenta.

[9]  Ewald R. Weibel,et al.  CORRELATED MORPHOMETRIC AND BIOCHEMICAL STUDIES ON THE LIVER CELL , 1969, The Journal of cell biology.

[10]  T. Mayhew,et al.  The new stereological methods for interpreting functional morphology from slices of cells and organs , 1991, Experimental Physiology.

[11]  M. Kantarci,et al.  Stereological evaluation of liver volume in living donor liver transplantation using MDCT via the cavalieri method , 2007, Liver transplantation : official publication of the American Association for the Study of Liver Diseases and the International Liver Transplantation Society.

[12]  M. Ochs,et al.  A brief update on lung stereology , 2006, Journal of microscopy.

[13]  E. Weibel,et al.  A MORPHOMETRIC STUDY OF THE REMOVAL OF PHENOBARBITAL-INDUCED MEMBRANES FROM HEPATOCYTES AFTER CESSATION OF TREATMENT , 1973, The Journal of cell biology.

[14]  H. J. G. GUNDERSEN,et al.  Some new, simple and efficient stereological methods and their use in pathological research and diagnosis , 1988, APMIS : acta pathologica, microbiologica, et immunologica Scandinavica.

[15]  A. Reith,et al.  Comparison of semiautomatic digitizer-tablet and simple point counting performance in morphometry , 1981, Virchows Archiv. B, Cell pathology including molecular pathology.

[16]  V. Brusasco,et al.  Stereology: a bridge to a better understanding of lung structure and function , 2010, European Respiratory Journal.

[17]  Wolfgang Kummer,et al.  Three-dimensional imaging and morphometric analysis of alveolar tissue from microfocal X-ray-computed tomography. , 2006, American journal of physiology. Lung cellular and molecular physiology.

[18]  Matthias Ochs,et al.  How much is there really? Why stereology is essential in lung morphometry. , 2007, Journal of applied physiology.

[19]  R. Østerby,et al.  Optimizing sampling efficiency of stereological studies in biology: or ‘Do more less well!‘ , 1981, Journal of microscopy.

[20]  K M Madsen,et al.  The art of counting. , 1999, Journal of the American Society of Nephrology : JASN.

[21]  H. Gundersen,et al.  Notes on the estimation of the numerical density of arbitrary profiles: the edge effect , 1977 .

[22]  S E Reichenbach,et al.  Evaluation of automated threshold selection methods for accurately sizing microscopic fluorescent cells by image analysis , 1989, Applied and environmental microbiology.

[23]  Rogely Waite Boyce,et al.  Design-based Stereology , 2010, Toxicologic pathology.

[24]  H. Gundersen,et al.  The efficiency of systematic sampling in stereology — reconsidered , 1999, Journal of microscopy.

[25]  Neil Roberts,et al.  Quantitative MRI of the prefrontal cortex and executive function in patients with temporal lobe epilepsy , 2009, Epilepsy & Behavior.

[26]  E R Weibel,et al.  Recent stereological methods for cell biology: a brief survey. , 1990, The American journal of physiology.

[27]  D. C. Sterio.  The unbiased estimation of number and sizes of arbitrary particles using the disector , 1984, Journal of microscopy.

[28]  Konrad Sandau,et al.  Unbiased Stereology. Three‐Dimensional Measurement in Microscopy. , 1999 .

[29]  L M Cruz-Orive,et al.  Sampling designs for stereology * , 1981, Journal of microscopy.

[30]  E. Weibel,et al.  Estimating length density and quantifying anisotropy in skeletal muscle capillaries , 1983, Journal of microscopy.

[31]  L M Cruz-Orive,et al.  Measuring error and sampling variation in stereology: comparison of the efficiency of various methods for planar image analysis , 1981, Journal of microscopy.

[32]  W. Scherle,et al.  A simple method for volumetry of organs in quantitative stereology. , 1970, Mikroskopie.

[33]  L M Cruz-Orive,et al.  Estimation of surface area from vertical sections , 1986, Journal of microscopy.

[34]  E. Weibel,et al.  PRACTICAL STEREOLOGICAL METHODS FOR MORPHOMETRIC CYTOLOGY , 1966, The Journal of cell biology.

[35]  E. Weibel,et al.  American Thoracic Society Documents An Official Research Policy Statement of the American Thoracic Society/European Respiratory Society: Standards for Quantitative Assessment of Lung Structure , 2010 .

[36]  H. J. G. Gundersen,et al.  The impact of recent stereological advances on quantitative studies of the nervous system , 1986, Journal of Neuroscience Methods.

[37]  L M Cruz-Orive,et al.  Precision of Cavalieri sections and slices with local errors , 1999, Journal of microscopy.